Commit 375bccae authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

POD corrections

parent 6053497d
......@@ -709,7 +709,6 @@ sub component_CoordSystem {
=head2 adaptor
Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor $adaptor
Example : none
Description: get/set for this objects database adaptor
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : none
......@@ -727,7 +726,7 @@ sub adaptor {
=head2 in_assembly
Description: Deprecated. Use map() or list_ids() instead
Deprecated. Use map() or list_ids() instead
=cut
......@@ -752,7 +751,7 @@ sub in_assembly {
=head2 map_coordinates_to_assembly
Description: DEPRECATED use map() instead
DEPRECATED use map() instead
=cut
......@@ -770,7 +769,7 @@ sub map_coordinates_to_assembly {
=head2 fast_to_assembly
Description: DEPRECATED use map() instead
DEPRECATED use map() instead
=cut
......@@ -787,7 +786,7 @@ sub fast_to_assembly {
=head2 map_coordinates_to_rawcontig
Description: DEPRECATED use map() instead
DEPRECATED use map() instead
=cut
......@@ -802,7 +801,7 @@ sub map_coordinates_to_rawcontig {
}
=head2 list_contig_ids
Description: DEPRECATED Use list_ids instead
DEPRECATED Use list_ids instead
=cut
......
......@@ -3708,7 +3708,7 @@ sub is_circular {
=head2 get_all_supercontig_Slices
Description: DEPRECATED use get_tiling_path("NTcontig") instead
DEPRECATED use get_tiling_path("NTcontig") instead
=cut
......@@ -3739,9 +3739,8 @@ sub get_all_supercontig_Slices {
=head2 get_Chromosome
Description: DEPRECATED use this instead:
$slice_adp->fetch_by_region('chromosome',
$slice->seq_region_name)
DEPRECATED use this instead:
$slice_adp->fetch_by_region('chromosome',$slice->seq_region_name)
=cut
......@@ -3762,7 +3761,7 @@ sub get_Chromosome {
=head2 chr_name
Description: DEPRECATED use seq_region_name() instead
DEPRECATED use seq_region_name() instead
=cut
......@@ -3773,7 +3772,7 @@ sub chr_name {
=head2 chr_start
Description: DEPRECATED use start() instead
DEPRECATED use start() instead
=cut
......@@ -3784,7 +3783,8 @@ sub chr_start {
=head2 chr_end
Description: DEPRECATED use end() instead
DEPRECATED use end() instead
Returntype : int
Exceptions : none
Caller : SliceAdaptor, general
......@@ -3798,7 +3798,7 @@ sub chr_end {
=head2 assembly_type
Description: DEPRECATED use version instead
DEPRECATED use version instead
=cut
......@@ -3810,7 +3810,7 @@ sub assembly_type {
=head2 get_tiling_path
Description: DEPRECATED use project instead
DEPRECATED use project instead
=cut
......@@ -3838,7 +3838,7 @@ sub dbID {
=head2 get_all_MapFrags
Description: DEPRECATED use get_all_MiscFeatures instead
DEPRECATED use get_all_MiscFeatures instead
=cut
......@@ -3850,7 +3850,7 @@ sub get_all_MapFrags {
=head2 has_MapSet
Description: DEPRECATED use get_all_MiscFeatures instead
DEPRECATED use get_all_MiscFeatures instead
=cut
......
......@@ -288,7 +288,7 @@ sub equals {
which is stored in the database, but it is a placeholder that
can be used to request transformations or retrievals to/from
the highest defined coordinate system in a given region.
Returntype : 0 or 1
Returntype : 1 or 0
Exceptions : none
Caller : general
Status : Stable
......@@ -306,7 +306,7 @@ sub is_top_level {
Arg [1] : none
Example : if($coord_sys->is_sequence_level()) { ... }
Description: Returns true if this is a sequence level coordinate system
Returntype : 0 or 1
Returntype : 1 or 0
Exceptions : none
Caller : general
Status : Stable
......@@ -325,7 +325,7 @@ sub is_sequence_level {
Example : if($coord_sys->is_default()) { ... }
Description: Returns true if this coordinate system is the default
version of the coordinate system of this name.
Returntype : 0 or 1
Returntype : 1 or 0
Exceptions : none
Caller : general
Status : Stable
......
......@@ -23,8 +23,6 @@
Bio::EnsEMBL::DBEntry -
Object representing an external reference (xref)
=head1 SYNOPSIS
=head1 DESCRIPTION
This object holds information about external references (xrefs) to
......@@ -493,9 +491,8 @@ sub type {
=head2 secondary_db_name
Arg [1] : String $secondary_db_name
Example : none
Description: Getter/setter for attribute 'secondary_db_name'.
Returnsecondary_db_name : String
Returntype : String
Exceptions : none
Caller : general
......@@ -513,9 +510,8 @@ sub secondary_db_name {
=head2 secondary_db_table
Arg [1] : String $secondary_db_table
Example : none
Description: Getter/setter for attribute 'secondary_db_table'.
Returnsecondary_db_table : String
Returns : String
Exceptions : none
Caller : general
......@@ -533,7 +529,6 @@ sub secondary_db_table {
=head2 add_synonym
Arg [1] : String $arg - synonym to add
Example : none
Description: Add a synonym for the external object.
Returntype : none
Exceptions : none
......@@ -623,7 +618,6 @@ sub get_all_masters {
=head2 flush_synonyms
Args : none
Example : none
Description: Remove all synonyms from this object.
Returntype : none
Exceptions : none
......@@ -641,7 +635,6 @@ sub flush_synonyms {
=head2 status
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute 'status'.
Returntype : String
Exceptions : none
......@@ -662,7 +655,6 @@ sub status{
=head2 ensembl_object_type
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute ensembl_object_type.
Returntype : String
Exceptions : none
......@@ -683,7 +675,6 @@ sub ensembl_object_type{
=head2 ensembl_id
Arg [1] : (optional) String $arg - value to set
Example : none
Description: Getter/setter for attribute ensembl_id.
Returntype : String
Exceptions : none
......@@ -709,7 +700,7 @@ sub ensembl_id{
=head2 get_synonyms
Description: DEPRECATED use get_all_synonyms instead
DEPRECATED use get_all_synonyms instead
=cut
......
......@@ -158,7 +158,7 @@ sub initialise_filehandle{
Arg[2] : int - seq_region_id
Arg[3] : int - seq_region offset. The byte offset required to
locate the required start position
Argp4[ : int - byte length to read
Arg[4] : int - byte length to read
Example : my $blob_substr = $self->read_collection_blob($filepath,
$sr_key,
$sr_offset,
......
......@@ -70,11 +70,11 @@ sub new_fast {
=head2 get_ExternalAdaptor
Arg[1] : Scalar; optional base path. Uses defaults if not given
Example : my $ea = $df->get_ExternalAdaptor('/base/path');
Example : my $ea = $df->get_ExternalAdaptor('/base/path');
Description : Delegates to the parent adaptor to retrieve the external
adaptor for this data type
Returntype : Any; will be an adaptor that can read the given data file
Exceptions : Thrown if there is no attached adaptor. Otherwise
adaptor for this data type
Returntype : Adaptor; will be an adaptor that can read the given data file
Exceptions : Thrown if there is no attached adaptor.
=cut
......@@ -89,19 +89,19 @@ sub get_ExternalAdaptor {
Arg[1] : Scalar base of the path to use. Can be ignored if the instance
already represents a canonical path
Example : my $f = $df->path();
Description : Used to generate the path to the file resource. Can return a
Example : my $f = $df->path();
Description : Used to generate the path to the file resource. Can return a
path to the file or a URL but it is up to the using code to
know how to interprate the different returned forms.
If the data file url is canonical then this is just returned.
If not then a path is generated of the form
B</base/path/production_name/coord_system_version/[software_version/]db_group/name.ext>
B</base/path/production_name/coord_system_version/[software_version]/db_group/name.ext>
Returntype : Scalar the absolute path/url to the given resource
Exceptions : Thrown if the linked Coordinate System lacks a version and the
Returntype : Scalar the absolute path/url to the given resource
Exceptions : Thrown if the linked Coordinate System lacks a version and the
current database also lacks a default version
Caller : public
Caller : public
=cut
......@@ -170,9 +170,9 @@ sub get_all_paths {
=head2 coord_system
Arg[1] : Bio::EnsEMBL::CoordSystem Optional setter
Description : Mutator for the coord system field. All files are linked to one
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : Thrown if not of the expected type
Description : Mutator for the coord system field. All files are linked to one
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : Thrown if not of the expected type
=cut
......
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